Cloning Git Repo for a stack doesn't copy over config files

Not sure if this should be happening, I have a docker compose file that uses several containers, two of these containers have configuration files (nginx being one of them) and are defined in the compose file.

However when I use portainer with the git repo option these config files do not come down, the folder structure does (as seen by CLI’ing onto the container)

Any ideas how to resolve this?

Compose File
version: ‘2’

services:
nginx:
image: nginx:1.13.12
ports:
- “443:443”
- “80:80”
volumes:
- ./:/var/www
- ./docker/nginxconf:/etc/nginx/conf.d
- ./docker/ssl-cert:/etc/nginx/certs
working_dir: /var/www
links:
- php
- mail
php:
build:
context: ./
dockerfile: docker/app.docker
volumes:
- ./:/var/www
depends_on:
- db
links:
- db
- mail
environment:
- “DB_PORT=3306”
- “DB_HOST=db”
db:
image: mariadb
environment:
- “MYSQL_ROOT_PASSWORD=removed
- “MYSQL_DATABASE=removed
ports:
- “33061:3306”

On another note, the files are found in the portainer container which is located on another server (using remote deploy via docker api)